presto.IO¶
File I/O and logging functions
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presto.IO.
countSeqFile
(seq_file)¶ Counts the records in FASTA/FASTQ files
Parameters: seq_file – FASTA or FASTQ file containing sample sequences Returns: Count of records in the sequence file Return type: int
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presto.IO.
countSeqSets
(seq_file, field='BARCODE', delimiter=('|', '=', ', '))¶ Identifies sets of sequences with the same ID field
Parameters: - seq_file – FASTA or FASTQ file containing sample sequences
- field – Annotation field containing set IDs
- delimiter – Tuple of delimiters for (fields, values, value lists)
Returns: Count of unit set IDs in the sequence file
Return type:
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presto.IO.
getFileType
(filename)¶ Determines the type of a file by file extension
Parameters: filename – Filename Returns: String defining the sequence type for SeqIO operations Return type: str
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presto.IO.
getOutputHandle
(in_file, out_label=None, out_dir=None, out_name=None, out_type=None)¶ Opens an output file handle
Parameters: - in_file – Input filename
- out_label – Text to be inserted before the file extension; if None do not add a label
- out_type – the file extension of the output file; if None use input file extension
- out_dir – the output directory; if None use directory of input file
- out_name – the short filename to use for the output file; if None use input file short name
Returns: File handle
Return type: file
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presto.IO.
printCount
(current, step, start_time=None, task=None, end=False)¶ Prints a progress bar to standard out
Parameters: - current (int) – count of completed tasks.
- step (int) – an int defining the progress increment to print at.
- start_time (time.time) – task start time returned by time.time(); if None do not add run time to progress
- task (str) – name of task to display.
- end (bool) – if True print final log (add newline).
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presto.IO.
printDebug
(message, debug=True)¶ Prints a debug message to standard error
Parameters:
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presto.IO.
printError
(message, exit=True)¶ Prints an error to standard error and exits
Parameters:
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presto.IO.
printLog
(record, handle=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, inset=None)¶ Formats a dictionary into a log string
Parameters: - record – a dict or OrderedDict of field names mapping to values.
- handle – the file handle to write the log to; if None do not write to file.
- inset – minimum field name inset; if None automatically space field names.
Returns: Formatted multi-line string in the log format.
Return type:
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presto.IO.
printMessage
(message, start_time=None, end=False, width=25)¶ Prints a progress message to standard out
Parameters: - message – Current task message
- start_time – task start time returned by time.time(); if None do not add run time to progress
- end – If True print final message (add newline)
- width – Maximum number of characters for messages
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presto.IO.
printProgress
(current, total, step, start_time=None, task=None, end=False)¶ Prints a progress bar to standard out
Parameters: - current (int) – count of completed tasks.
- total (int) – total task count.
- step (float) – float defining the fractional progress increment to print at.
- start_time (float) – task start time returned by time.time(); if None do not add run time to progress
- task (str) – name of task to display.
- end (bool) – if True print final log (add newline).
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presto.IO.
printWarning
(message)¶ Prints a warning to standard error
Parameters: message (str) – warning message.
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presto.IO.
readPrimerFile
(primer_file)¶ Processes primer sequences from file
Parameters: primer_file (str) – name of the FASTA file containing primer sequences. Returns: Dictionary mapping primer ID to sequence. Return type: dict
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presto.IO.
readReferenceFile
(ref_file)¶ Create a dictionary of cleaned and ungapped reference sequences.
Parameters: ref_file – reference sequences in fasta format. Returns: - cleaned and ungapped reference sequences;
- with the key as the sequence ID and value as a Bio.SeqRecord for each reference sequence.
Return type: dict
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presto.IO.
readSeqFile
(seq_file, index=False, key_func=None)¶ Reads FASTA/FASTQ files
Parameters: - seq_file – FASTA or FASTQ file containing sample sequences
- index – If True return a dictionary from SeqIO.index(); if False return an iterator from SeqIO.parse()
- key_func – the key_function argument to pass to SeqIO.index if index=True
Returns: an interator of SeqRecords if index=False. A dict if True.
Return type: iter